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DNA variants in or close to the human  TBX15  and  PAX1  genes have been repeatedly associated with facial morphology in independent genome‐wide association studies, while their functional roles in determining facial morphology remain to be understood. We generated  Tbx15  knockout ( Tbx15  −/− ) and  Pax1  knockout ( Pax1  −/− ) mice by applying the one‐step CRISPR/Cas9 method. A total of 75 adult mice were used for subsequent phenotype analysis, including 38  Tbx15  mice (10 homozygous  Tbx15  −/− , 18 heterozygous  Tbx15  +/− , 10 wild‐type  Tbx15  +/+   WT  littermates) and 37  Pax1  mice (12 homozygous  Pax1  −/− , 15 heterozygous  Pax1  +/− , 10  Pax1  +/+   WT  littermates). Facial and other physical morphological phenotypes were obtained from three‐dimensional (3D) images acquired with the HandySCAN BLACK scanner. Compared to  WT  littermates, the  Tbx15  −/−  mutant mice had significantly shorter faces ( p  = 1.08E‐8, R 2  = 0.61) and their ears were in a significantly lower position ( p  = 3.54E‐8, R 2  = 0.62) manifesting a “droopy ear” characteristic. Besides these face alternations,  Tbx15  −/−  mutant mice displayed significantly lower weight as well as shorter body and limb length.  Pax1  −/−  mutant mice showed significantly longer noses ( p  = 1.14E‐5, R 2  = 0.46) relative to  WT  littermates, but otherwise displayed less obvious morphological alterations than  Tbx15  −/−  mutant mice did. We provide the first direct functional evidence that two well‐known and replicated human face genes,  Tbx15  and  Pax1 , impact facial and other body morphology in mice. The general agreement between our findings in knock‐out mice with those from previous GWASs suggests that the functional evidence we established here in mice may also be relevant in humans.

The effects of Tbx15 and Pax1 on facial and other physical morphology in mice